Hi Knut

in the bert aseg I have for coronal slice 114 the none is correct - it's outside the brain I think.

Bruce On Mon, 21 Jan 2013, Knut J Bjuland wrote:

Hi Bruce,

I found a None segmentation between left hippocampus and left ventral DC in Bert, which is similar to none segmentation in the hippocampus in mine subjects. Should I been concerned about this type of segmentation error in hippocampus and thalamus. I found this none segmentation in Bert at coronal slice 114. Is there any guide line on how much none segmentation that is allowed? I have used the Bert subject as atlas.

Knut J

On 01/21/2013 03:22 PM, Bruce Fischl wrote:

...

Hi Knut,

I'm not positive what you mean, but if you want None voxels that are adjacent to hippocampus you could use mri_morphometry to dilate each hippocampus, then do the rest in 3-4 lines of matlab. Something like

[vol_lh_dilated,M,mr] = load_mgh('lh.hippo.dilated.mgz') ; [vol_lh,M,mr] = load_mgh('aseg.mgz') ;

ind = find(vol_lh_dilated == 17 & vol_lh == 0);

although you may need to binarize, in which case you would replace the 17 above with 1.

cheers Bruce

On Mon, 21 Jan 2013, Knut J Bjuland wrote:

...

Hi,

How can I calculate the number of None segmentation in right or left hippocampus or another structure in Matlab or in Freesufer?

Knut J

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